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- PDB-6ohh: Structure of EF1p2_mFAP2b bound to DFHBI -

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Basic information

Entry
Database: PDB / ID: 6ohh
TitleStructure of EF1p2_mFAP2b bound to DFHBI
ComponentsEF1p2_mFAP2b
KeywordsDE NOVO PROTEIN / Rossetta / ligand binder / computational / beta barrel / EF-motif
Function / homologyChem-38E
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsDoyle, L.A. / Stoddard, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM115545 United States
CitationJournal: Nat Commun / Year: 2021
Title: Incorporation of sensing modalities into de novo designed fluorescence-activating proteins
Authors: Klima, J.C. / Doyle, L.A. / Lee, J.D. / Rappleye, M. / Gagnon, L.A. / Lee, M.Y. / Barros, E.P. / Vorobieva, A.A. / Dou, J. / Bremner, S. / Jacob, S. / Quon, J.S. / Chow, C.M. / Carter, L. / ...Authors: Klima, J.C. / Doyle, L.A. / Lee, J.D. / Rappleye, M. / Gagnon, L.A. / Lee, M.Y. / Barros, E.P. / Vorobieva, A.A. / Dou, J. / Bremner, S. / Jacob, S. / Quon, J.S. / Chow, C.M. / Carter, L. / Mack, D.L. / Amaro, R.E. / Vaughan, J.C. / Berndt, A. / Stoddard, B.L. / Baker, D.
History
DepositionApr 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EF1p2_mFAP2b
B: EF1p2_mFAP2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4576
Polymers27,8732
Non-polymers5854
Water3,927218
1
A: EF1p2_mFAP2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2293
Polymers13,9361
Non-polymers2922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EF1p2_mFAP2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2293
Polymers13,9361
Non-polymers2922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.350, 35.564, 86.596
Angle α, β, γ (deg.)90.000, 90.680, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 3 and (name N or name...
21(chain B and (resid 3 through 5 or (resid 6...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSER(chain A and ((resid 3 and (name N or name...AA33
12SERSERGLNGLN(chain A and ((resid 3 and (name N or name...AA3 - 1283 - 128
13SERSERGLNGLN(chain A and ((resid 3 and (name N or name...AA3 - 1283 - 128
14SERSERGLNGLN(chain A and ((resid 3 and (name N or name...AA3 - 1283 - 128
15SERSERGLNGLN(chain A and ((resid 3 and (name N or name...AA3 - 1283 - 128
21SERSERSERSER(chain B and (resid 3 through 5 or (resid 6...BB3 - 53 - 5
22ARGARGARGARG(chain B and (resid 3 through 5 or (resid 6...BB66
23GLYGLYGLNGLN(chain B and (resid 3 through 5 or (resid 6...BB1 - 1281 - 128
24GLYGLYGLNGLN(chain B and (resid 3 through 5 or (resid 6...BB1 - 1281 - 128
25GLYGLYGLNGLN(chain B and (resid 3 through 5 or (resid 6...BB1 - 1281 - 128
26GLYGLYGLNGLN(chain B and (resid 3 through 5 or (resid 6...BB1 - 1281 - 128
27GLYGLYGLNGLN(chain B and (resid 3 through 5 or (resid 6...BB1 - 1281 - 128
28GLYGLYGLNGLN(chain B and (resid 3 through 5 or (resid 6...BB1 - 1281 - 128

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Components

#1: Protein EF1p2_mFAP2b


Mass: 13936.296 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-38E / (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one


Mass: 252.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10F2N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 13, 2018 / Details: Confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 13078 / % possible obs: 98.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.025 / Rpim(I) all: 0.016 / Rrim(I) all: 0.03 / Χ2: 0.595 / Net I/σ(I): 16.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.142.80.0555700.9960.040.0680.58786.2
2.14-2.183.30.0596100.9970.0390.0710.60696.5
2.18-2.223.60.066740.9960.0360.070.61199.3
2.22-2.263.60.0556290.9970.0340.0650.7299.5
2.26-2.313.70.0566510.9970.0340.0650.60299.1
2.31-2.373.60.0476470.9980.0280.0550.58499.1
2.37-2.423.60.0476700.9970.0290.0560.62499.6
2.42-2.493.70.0436200.9980.0260.0510.56699.4
2.49-2.563.70.0426730.9980.0260.0490.5899.7
2.56-2.653.60.0366480.9990.0220.0430.5999.7
2.65-2.743.70.0336610.9990.020.0390.585100
2.74-2.853.70.0326540.9980.020.0380.581100
2.85-2.983.70.036670.9990.0180.0350.566100
2.98-3.143.70.0246480.9990.0140.0280.52100
3.14-3.333.70.0236760.9990.0140.0270.569100
3.33-3.593.70.026640.9990.0120.0240.543100
3.59-3.953.70.0196660.9990.0110.0220.58100
3.95-4.523.60.01767210.010.020.519100
4.52-5.693.70.01867210.0110.0210.583100
5.69-303.50.0270610.0120.0230.7999.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.1 Å25.42 Å
Translation2.1 Å25.42 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.7.16phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→25.42 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.82
RfactorNum. reflection% reflection
Rfree0.2009 1314 10.06 %
Rwork0.1692 --
obs0.1725 13060 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 46.19 Å2 / Biso mean: 20.1378 Å2 / Biso min: 9.28 Å2
Refinement stepCycle: final / Resolution: 2.1→25.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 38 218 2144
Biso mean--14.58 27.9 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041985
X-RAY DIFFRACTIONf_angle_d0.8592712
X-RAY DIFFRACTIONf_chiral_restr0.056292
X-RAY DIFFRACTIONf_plane_restr0.006357
X-RAY DIFFRACTIONf_dihedral_angle_d2.4661351
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1066X-RAY DIFFRACTION7.776TORSIONAL
12B1066X-RAY DIFFRACTION7.776TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0994-2.18340.22651300.17581191132192
2.1834-2.28270.24581550.17891298145399
2.2827-2.40290.22311300.18731313144399
2.4029-2.55340.2061470.19281304145199
2.5534-2.75030.23011500.190613001450100
2.7503-3.02670.20031450.195113291474100
3.0267-3.46370.18791450.167713101455100
3.4637-4.36030.17531480.143413341482100
4.3603-25.42190.19191640.149613671531100

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